| 1. |
- Alves, Luis, et al.
(author)
-
New Insights on the Role of Urea on the Dissolution and Thermally-Induced Gelation of Cellulose in Aqueous Alkali
- 2018
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In: GELS. - : MDPI AG. - 2310-2861. ; 4:4
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Journal article (peer-reviewed)abstract
- The gelation of cellulose in alkali solutions is quite relevant, but still a poorly understood process. Moreover, the role of certain additives, such as urea, is not consensual among the community. Therefore, in this work, an unusual set of characterization methods for cellulose solutions, such as cryo-transmission electronic microscopy (cryo-TEM), polarization transfer solid-state nuclear magnetic resonance (PTssNMR) and diffusion wave spectroscopy (DWS) were employed to study the role of urea on the dissolution and gelation processes of cellulose in aqueous alkali. Cryo-TEM reveals that the addition of urea generally reduces the presence of undissolved cellulose fibrils in solution. These results are consistent with PTssNMR data, which show the reduction and in some cases the absence of crystalline portions of cellulose in solution, suggesting a pronounced positive effect of the urea on the dissolution efficiency of cellulose. Both conventional mechanical macrorheology and microrheology (DWS) indicate a significant delay of gelation induced by urea, being absent until ca. 60 degrees C for a system containing 5wt % cellulose, while a system without urea gels at a lower temperature. For higher cellulose concentrations, the samples containing urea form gels even at room temperature. It is argued that since urea facilitates cellulose dissolution, the high entanglement of the cellulose chains in solution (above the critical concentration, C*) results in a strong three-dimensional network.
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| 2. |
- Melro, Elodie, et al.
(author)
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Dissolution of kraft lignin in alkaline solutions
- 2020
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In: International Journal of Biological Macromolecules. - : Elsevier BV. - 0141-8130 .- 1879-0003. ; 148, s. 688-695
-
Journal article (peer-reviewed)abstract
- Lignins are among the most abundant renewable resources on the planet. However, their application is limited by the lack of efficient dissolution and extraction methodologies. In this work, a systematic and quantitative analysis of the dissolution efficiency of different alkaline-based aqueous systems (i.e. lithium hydroxide, LiOH; sodium hydroxide, NaOH; potassium hydroxide, KOH; cuprammonium hydroxide, CuAOH; tetrapropylammonium hydroxide, TPAOH and tetrabutylammonium hydroxide, TBAOH) is reported, for the first time, for kraft lignin. Phase maps were determined for all systems and lignin solubility was found to decrease in the following order: LiOH > NaOH > KOH > CuAOH > TPAOH > TBAOH, thus suggesting that the size of the cation plays an important role on its solubility. The π∗ parameter has an opposite trend to the solubility, supporting the idea that cations of smaller size favor lignin solubility. Dissolution was observed to increase exponentially above pH 9–10 being the LiOH system the most efficient. The soluble and insoluble fractions of lignin in 0.1 M NaOH were collected and analyzed by several techniques. Overall, data suggests a greater amount of simple aromatic compounds, preferentially containing sulfur, in the soluble fraction while the insoluble fraction is very similar to the native kraft lignin.
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| 3. |
- Melro, Elodie, et al.
(author)
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Levulinic acid : A novel sustainable solvent for lignin dissolution
- 2020
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In: International Journal of Biological Macromolecules. - : Elsevier BV. - 0141-8130 .- 1879-0003. ; 164, s. 3454-3461
-
Journal article (peer-reviewed)abstract
- Lignin is a natural, renewable resource with potential to be used in biomaterials. Due to its complex structure, its efficient dissolution is still challenging, which hinders its applicability at large scale. This challenge become harder considering the current need of sustainable and environmentally friendly solvents. To the best of our knowledge, this work reports for the first time the dissolution of kraft lignin in levulinic acid, a “green” solvent, and compares its efficiency with common carboxylic acids and sulfuric acid. It has been found that levulinic acid has a high capacity to dissolve kraft lignin at room temperature (40 wt% solubility), and it efficiency is not compromised when diluting the acid with water (up to 40 wt% water content). The Kamlet-Taft π⁎ parameter of the different acidic solvents was estimated and found to correlate well with their solubility performance. Lignins previously dissolved in levulinic and formic acids were selected to be regenerated and minor differences were found in thermal stability and morphological structure, when compared to native kraft lignin. However, an increase in the content of the carbonyl groups in the regenerated lignin material was observed.
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| 4. |
- Alves, Luis, et al.
(author)
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Revisiting the dissolution of cellulose in H3PO4(aq) through cryo-TEM, PTssNMR and DWS
- 2021
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In: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617 .- 1879-1344. ; 252
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Journal article (peer-reviewed)abstract
- Cellulose can be dissolved in concentrated acidic aqueous solvents forming extremely viscous solutions, and, in some cases, liquid crystalline phases. In this work, the concentrated phosphoric acid aqueous solvent is revisited implementing a set of advanced techniques, such as cryo-transmission electronic microscopy (cryo-TEM), polarization transfer solid-state nuclear magnetic resonance (PTssNMR), and diffusing wave spectroscopy (DWS). Cryo-TEM images confirm that this solvent system is capable to efficiently dissolve cellulose. No cellulose particles, fibrils, or aggregates are visible. Conversely, PTssNMR revealed a dominant CP signal at 25 °C, characteristic of C-H bond reorientation with correlation time longer than 100 ns and/or order parameter above 0.5, which was ascribed to a transient gel-like network or an anisotropic liquid crystalline phase. Increasing the temperature leads to a gradual transition from CP to INEPT-dominant signal and a loss of birefringence in optical microscopy, suggesting an anisotropic-to-isotropic phase transition. Finally, an excellent agreement between optical microrheology and conventional mechanical rheometry was also obtained.
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| 5. |
- Ascic, Ervin, et al.
(author)
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Eliciting Anti-Tumor Immunity by Reprogramming Cancer Cells to Type 1 Conventional Dendritic Cells
- 2022
-
Conference paper (other academic/artistic)abstract
- IntroductionAn important hallmark of cancer is escaping the immune system. Despite advances in immunotherapy, only a subset of patients experiences clinical benefits. It was shown that adoptive T cell or checkpoint inhibition therapy rely on the presence of conventional dendritic cells type 1 (cDC1). cDC1 excel in recruiting and priming protective CD8+ T cells through cross-presentation. However, in tumors cDC1 are often impaired in function. Recently, we demonstrated that overexpression of PU.1, IRF8 and BATF3 (PIB) imposes a cDC1 fate in fibroblasts by direct cell reprogramming. As such, we hypothesise that a similar combination of transcription factors would reprogram cancer cells into tumor-antigen presenting cells (tumor-APCs) and set in motion antigen-specific immunity.Material and Methods30 mouse tumor lines were selected to evaluate reprogramming into tumor-APCs. Reprogramming was induced by overexpression of PIB via lentiviral transduction. The phenotype was profiled by flow cytometry for cDC1 markers CD45, MHC-II, CLEC9A, XCR1 and APC markers MHC-I, CD80/86. Population mRNA-seq was applied to assess transcriptional changes. To assess cDC1 functions, cytokine secretion, cross-presentation and T cell cytotoxicity assays were performed. In vivo, ovalbumin expressing tumors were established and treated by adoptive transfer of tumor-APCs. Tumor growth and animal survival were monitored.Results and DiscussionsUpon transduction with PIB, 26 solid tumor and 4 leukemia lines initiated expression of CD45, MHC-II, at efficiencies ranging from 0.5-57.7%. Reprogramming was accompanied by CLEC9A, XCR1 and MHC-I, CD80/86 upregulation. Transcriptomic analysis of low immunogenic lines B16 and LLC, reveals that PIB overwrites the cancer transcriptome and imposes antigen presentation and cDC1 gene signatures. Importantly, tumor-APCs present endogenous antigens on MHC-I and become prone to T cell mediated killing. Functionally, reprogrammed tumor-APCs secrete inflammatory cytokines such as IL12p70 and strikingly, acquire the ability to crosspresent antigens and prime naïve CD8+ T cells. In vivo, adoptive transfer of cross-presenting tumor-APCs delays tumor growth and extends survival of animals.ConclusionThis approach combines cDC1 antigen presentation abilities with endogenous generation of tumor antigens. The induction of a cDC1 identity in tumor cells sets in motion T cell responses and makes them target for T cell mediated killing. Our study represents a pioneering contribution merging cell reprogramming with immunotherapy.
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| 6. |
- Ascic, Ervin, et al.
(author)
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Harnessing Dendritic Cell Reprogramming to Elucidate Mechanisms of Tumor Immunity
- 2022
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Conference paper (other academic/artistic)abstract
- The presence of conventional dendritic cells type 1 (cDC1) in the tumor correlates with positive treatment outcome. The ability to cross-present neoantigens and prime protective CD8+ T-cell responses, makes cDC1s central for tumor immunity. However, in tumors cDC1 are rare and often functionally impaired. Our group reported that overexpression of the transcription factors PU.1, IRF8 and BATF3 (PIB) converts mouse and human fibroblasts into cross-presenting cDC1-like cells. We employed the minimal gene regulatory network of highly immunogenic cDC1 and restored the immunogenicity of low immunogenic lung cancer and melanoma cell lines by reprogramming into professional tumor antigen presenting cells (tumor-APCs). Here, we report that upon transduction with PIB, 23 solid syngeneic cancer lines initiate reprogramming into cDC1-like cells expressing CD45 and MHC-II at efficiencies ranging from 0.5-57.7%. Functionally, PIB overexpression endows tumor cells with the capacity to cross-present exogenous antigen and prime naïve CD8+ T-cells. Adoptive transfer of ovalbumin cross-presenting B16 tumor-APCs into established ovalbumin expressing B16 tumors (B16-OVA) elicits tumor growth control and extends animal survival. Treated animals show a systemic antigen-specific T cell response against ovalbumin and endogenous tumor-associated antigen MuLV p15E. Intratumoral injection of reprogrammed B2905 and LLC into tumors shows differential response, correlating with their cross-presentation capacity. This approach combines cDC1 antigen cross-presentation abilities with the generation of tumor antigens. The induction of a cDC1 identity in tumor cells sets in motion T cell responses in vitro and in vivo. In the future of this project, dendritic cell reprogramming will be object in a 2-cell CRISPR/Cas9 screen using induced cDC1-like tumor cells and reporter T-cells to explore mechanistically cross-presentation regulators. The generation of cross-presenting tumor-APCs will be also used to map and characterize presented and cross-presented neoantigens. Finally, dendritic cell reprogramming of tumor cells will be explored in vivo by replenishing cDC1 within the tumor microenvironment through in vivo reprogramming. Ultimately, this project will provide insight into mechanisms of cross-presentation and pave the way for the development of novel cDC1-centric therapies.
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| 7. |
- Costa, Carolina, et al.
(author)
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Cellulose-stabilized oil-in-water emulsions : Structural features, microrheology, and stability
- 2021
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In: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617 .- 1879-1344. ; 252
-
Journal article (peer-reviewed)abstract
- Cellulose-based oil-in-water (O/W) emulsions were studied by diffusing wave spectroscopy (DWS) regarding the effect of the cellulose concentration and mixing rate on the average droplet size, microrheological features and stability. Furthermore, the microstructure of these emulsions was imaged by cryo-scanning electron microscopy (cryo-SEM). The micrographs showed that cellulose was effectively adsorbed at the oil-water interface, resembling a film-like shell that protected the oil droplets from coalescing. The non-adsorbed cellulose that was observed in the continuous aqueous medium, contributed to the enhancement of the viscosity of the medium, leading to an improvement in the stability of the overall system. Generally, the higher the cellulose concentration and mixing rate, the smaller the emulsion droplets formed, and the higher was their stability. The combination of both techniques, DWS and cryo-SEM, revealed a very appealing and robust methodology for the characterization and design of novel emulsion-based formulations.
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| 8. |
- Costa, Carolina, et al.
(author)
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Emulsion Formation and Stabilization by Biomolecules : The Leading Role of Cellulose.
- 2019
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In: Polymers. - : MDPI AG. - 2073-4360. ; 11:10
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Journal article (peer-reviewed)abstract
- Emulsion stabilization by native cellulose has been mainly hampered because of its insolubility in water. Chemical modification is normally needed to obtain water-soluble cellulose derivatives. These modified celluloses have been widely used for a range of applications by the food, cosmetic, pharmaceutic, paint and construction industries. In most cases, the modified celluloses are used as rheology modifiers (thickeners) or as emulsifying agents. In the last decade, the structural features of cellulose have been revisited, with particular focus on its structural anisotropy (amphiphilicity) and the molecular interactions leading to its resistance to dissolution. The amphiphilic behavior of native cellulose is evidenced by its capacity to adsorb at the interface between oil and aqueous solvent solutions, thus being capable of stabilizing emulsions. In this overview, the fundamentals of emulsion formation and stabilization by biomolecules are briefly revisited before different aspects around the emerging role of cellulose as emulsion stabilizer are addressed in detail. Particular focus is given to systems stabilized by native cellulose, either molecularly-dissolved or not (Pickering-like effect).
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| 9. |
- Costa, Carolina, et al.
(author)
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On the formation and stability of cellulose-based emulsions in alkaline systems : Effect of the solvent quality
- 2022
-
In: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617 .- 1879-1344. ; 286
-
Journal article (peer-reviewed)abstract
- With amphiphilic properties, cellulose molecules are expected to adsorb at the O/W interface and be capable of stabilizing emulsions. The effect of solvent quality on the formation and stability of cellulose-based O/W emulsions was evaluated in different alkaline systems: NaOH, NaOH-urea and tetrabutylammonium hydroxide (TBAH). The optimal solvency conditions for cellulose adsorption at the O/W interface were found for the alkaline solvent with an intermediate polarity (NaOH-urea), which is in line with the favorable conditions for adsorption of an amphiphilic polymer. A very good solvency (in TBAH) and the interfacial activity of the cation lead to lack of stability because of low cellulose adsorption. However, to achieve long-term stability and prevent oil separation in NaOH-urea systems, further reduction in cellulose's solvency was needed, which was achieved by a change in the pH of the emulsions, inducing the regeneration of cellulose at the surface of the oil droplets (in-situ regeneration).
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| 10. |
- Ferreira, Alexandra G, et al.
(author)
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Reprogramming Cancer Cells to Antigen-presenting Cells
- 2023
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In: Bio-protocol. - 2331-8325. ; 13:22, s. 1-25
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Journal article (peer-reviewed)abstract
- Cancer cells evade the immune system by downregulating antigen presentation. Although immune checkpoint inhibitors (ICI) and adoptive T-cell therapies revolutionized cancer treatment, their efficacy relies on the intrinsic immunogenicity of tumor cells and antigen presentation by dendritic cells. Here, we describe a protocol to directly reprogram murine and human cancer cells into tumor-antigen-presenting cells (tumor-APCs), using the type 1 conventional dendritic cell (cDC1) transcription factors PU.1, IRF8, and BATF3 delivered by a lentiviral vector. Tumor-APCs acquire a cDC1 cell-like phenotype, transcriptional and epigenetic programs, and function within nine days (Zimmermannova et al., 2023). Tumor-APCs express the hematopoietic marker CD45 and acquire the antigen presentation complexes MHC class I and II as well as co-stimulatory molecules required for antigen presentation to T cells, but do not express high levels of negative immune checkpoint regulators. Enriched tumor-APCs present antigens to Naïve CD8 + and CD4 + T cells, are targeted by activated cytotoxic T lymphocytes, and elicit anti-tumor responses in vivo. The tumor-APC reprogramming protocol described here provides a simple and robust method to revert tumor evasion mechanisms by increasing antigen presentation in cancer cells. This platform has the potential to prime antigen-specific T-cell expansion, which can be leveraged for developing new cancer vaccines, neoantigen discovery, and expansion of tumor-infiltrating lymphocytes. Key features • This protocol describes the generation of antigen-presenting cells from cancer cells by direct reprogramming using lineage-instructive transcription factors of conventional dendritic cells type I. • Verification of reprogramming efficiency by flow cytometry and functional assessment of tumor-APCs by antigen presentation assays.
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| 11. |
- Ferreira, Alexandra Gabriela, et al.
(author)
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Restoring the immunogenicity of cancer cells with dendritic cell reprogramming
- 2021
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In: Experimental Hematology. - : Elsevier BV. - 1873-2399 .- 0301-472X. ; 100:Suppl, s. 72-72
-
Conference paper (peer-reviewed)abstract
- An important hallmark of cancer is the ability to evade the immune system. Genetic mutations may result in the accumulation of tumor antigens, however, downregulation of antigen presentation in tumor cells results in decreased immunogenicity and immune surveillance evasion. Recently, we demonstrated that enforced expression of PU.1, IRF8 and BATF3 (PIB) imposes a conventional dendritic cell type 1 (cDC1) fate in fibroblasts by direct cell reprogramming. As such, we hypothesise that a similar combination of transcription factors can reprogram cancer cells into antigen presenting cells.Here, we show that expression of PIB factors is sufficient to induce hematopoietic and cDC1 markers in the mouse melanoma and lung cancer cell lines B16 and 3LL. We further show that reprogramming restores the expression of antigen presentation molecules (MHC-II, MHC-I and B2M) at cancer cell surface. This is accompanied by the activation of the co-stimulatory molecules CD80 and CD86. This reprogrammed tumor antigen presenting cell (tumor-APC) phenotype is specified gradually within the course of 9 days. PIB overwrites the cancer transcriptional program imposing global antigen presentation and cDC1 gene signatures. Functionally, tumor-APCs secrete inflammatory cytokines such as IL-12, IL-6, CXCL10 and type 1 interferons. After reprogramming they also acquire the capacity to uptake and process proteins as well as dead cells. Importantly, tumor-APCs directly prime antigen-specific naïve CD8+ T-cells after antigen loading. Finally, tumor-APCs are capable to show endogenous antigens to T cells and become prone to T cell mediated cell killing.Our approach combines cDC1’s antigen processing and presenting abilities with the endogenous generation of tumor antigens, and serves as a platform for the development of novel immunotherapies based on endowed antigen presentation in cancer cells.
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| 12. |
- Ferreira, Alexandra Gabriela, et al.
(author)
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Restoring tumor immunogenicity with dendritic cell reprogramming
- 2022
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In: Cancer immunology research. - 2326-6074. ; 10:12 suppl
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Conference paper (peer-reviewed)abstract
- Immunotherapy is revolutionizing cancer treatment, but success is limited to a fraction of patients. Tumor immunosurveillance and immunotherapy relies on presentation of tumor-associated antigens by conventional dendritic cells type 1 (cDC1). However, tumors develop mechanisms to avoid immune recognition such as downregulation of antigen presentation and exclusion of cDC1. We have previously demonstrated that enforced expression of the transcription factors PU.1, IRF8 and BATF3 (PIB) imposes the lineage conversion of fibroblasts to cDC1 by direct cell reprogramming. Here, we hypothesize that PIB reprograms cancer cells directly into functional tumor-antigen presenting cells (tumor-APCs) with enhanced immunogenicity. First, we show that enforced expression of PIB in a wide range of murine and human cancer cells from different origins is sufficient to induce surface expression of hematopoietic and DC-lineage specific markers (CD45 and Clec9a). Moreover, reprogramming restored the expression of antigen presentation complexes (MHC-I and MHC-II) and activated the expression of the co-stimulatory molecules CD40, CD80 and CD86, required for productive T cell activation. Transcriptomic analysis using mRNA-sequencing showed that PIB imposes a global cDC1 gene signature and an antigen presentation program in tumor cells as early as day 3 of reprogramming, overriding the original cancer cell program. Furthermore, Assay for Transposase-Accessible Chromatin (ATAC) sequencing analysis revealed that PIB-mediated cDC1 reprogramming elicited rapid epigenetic remodeling followed by gradual rewiring of transcriptional program and stabilization of cDC1 identity. Functionally, tumor-APCs present endogenous antigens on MHC-I, prime naïve CD8+ T and become prone to CD8+ T cell mediated killing. Tumor-APCs secrete pro-inflammatory cytokines (IL-12) and chemoattractants (CXCL10), uptake and process exogenous antigens, phagocyte dead cells, and cross-present exogenous antigens to activate naïve T-cells. In addition, reprogrammed tumor cells harboring TP53, KRAS and PTEN mutations downregulated proliferation and showed impaired tumorigenicity in vitro and in vivo. Importantly, we show that intra-tumoral injection of reprogrammed tumor-APCs elicited tumour growth control in vivo alongside increasing infiltration of CD8+ T and NK cells in B16-OVA tumors. Finally, we showed that our approach can be employed to convert primary cancer cells derived from melanoma, lung, breast, pancreatic, urothelial, and head and neck carcinomas as well as cancer associated fibroblasts. In summary, we provide evidence for the direct reprogramming of tumor cells into immunogenic cDC1-like cells, with restored antigen presentation capacity and the ability to reinstate anti-tumor immunity. Our approach elicits the immune system against cancer and counteract major tumor evasion mechanisms including tumor heterogeneity and impaired antigen presentation, laying the foundation for developing immunotherapeutic strategies based on the cellular reprogramming of human cancer cells.
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| 13. |
- Fiúza Rosa, Fábio, et al.
(author)
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Direct Reprogramming of Mouse and Human Fibroblasts into Conventional Dendritic Cells Type 1
- 2022
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In: Molecular Immunology. - : Elsevier BV. - 1872-9142 .- 0161-5890. ; 150, s. 22-22
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Conference paper (peer-reviewed)abstract
- Cell fate reprogramming of adult cells towards pluripotency or unrelated somatic cell-types has been explored in the context of regenerative medicine. Dendritic cells (DCs) are professional antigen presenting cells (APCs) specialized in the recognition, processing and presentation of antigens to T-cells, inducing adaptive immunity. In particular, the mouse conventional DCs type 1 (cDC1) subset or DC1 human equivalent excel on the ability to perform antigen cross-presentation, a critical step for inducing cytotoxic responses. We hypothesized that the unique properties of cDC1s could be induced in unrelated cell-types, allowing the direct control of immune responses with cell reprogramming.Here, the requirements to induce cDC1s were investigated using combinatorial overexpression of Transcription Factors (TFs) in Clec9a-tdTomato mouse fibroblasts. In the hematopoietic system, Clec9a specifically marks the DC lineage, including all conventional dendritic cells type 1 (cDC1). We have identified PU.1, IRF8 and BATF3 (PIB) as sufficient and necessary to induce Clec9a reporter activation, establish DC morphology and activate a cDC1 transcriptional program in mouse fibroblasts. The over- expression of PIB ignites the expression of DC markers including CD103, XCR1, MHC-I, MHC-II and co-stimulatory molecules. Functionally, Induced DCs (iDCs) secrete inflammatory cytokines and engulf, process, present and cross-present antigens to CD4+ and CD8+ T cells, respectively. Additionally, we have demonstrated that combined expression of PIB factors induces DC1 reprogramming in human fibroblasts. Human iDC1s acquire DC morphology, express DC1 markers, including Clec9a, CD141 and the co-stimulatory molecules CD40, CD80 and CD86, and acquire a DC1 transcriptional signature at the single cell level. Interestingly, DC1 reprogramming efficiency can be enhanced 70-fold by supplementing culture media with inflammatory cytokines, suggesting a regulatory role of inflammation during DC1 reprogramming.Hence, we provide evidence that antigen presentation and cross-presentation can be dynamically programmed by a small combination of TFs. These findings provide insights into cDC1 specification and a platform for developing cancer immunotherapies based on cell reprogramming.
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| 14. |
- Fluet-Chouinard, Etienne, et al.
(author)
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Extensive global wetland loss over the past three centuries
- 2023
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 614:7947, s. 281-286
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Journal article (peer-reviewed)abstract
- Wetlands have long been drained for human use, thereby strongly affecting greenhouse gas fluxes, flood control, nutrient cycling and biodiversity1,2. Nevertheless, the global extent of natural wetland loss remains remarkably uncertain3. Here, we reconstruct the spatial distribution and timing of wetland loss through conversion to seven human land uses between 1700 and 2020, by combining national and subnational records of drainage and conversion with land-use maps and simulated wetland extents. We estimate that 3.4 million km2 (confidence interval 2.9–3.8) of inland wetlands have been lost since 1700, primarily for conversion to croplands. This net loss of 21% (confidence interval 16–23%) of global wetland area is lower than that suggested previously by extrapolations of data disproportionately from high-loss regions. Wetland loss has been concentrated in Europe, the United States and China, and rapidly expanded during the mid-twentieth century. Our reconstruction elucidates the timing and land-use drivers of global wetland losses, providing an improved historical baseline to guide assessment of wetland loss impact on Earth system processes, conservation planning to protect remaining wetlands and prioritization of sites for wetland restoration4.
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| 15. |
- Grant, Danielle M., et al.
(author)
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The future of dna barcoding : Reflections from early career researchers
- 2021
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In: Diversity. - : MDPI AG. - 1424-2818. ; 13:7
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Journal article (peer-reviewed)abstract
- Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.
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| 16. |
- Johnson, Eileanoir B, et al.
(author)
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Neurofilament light protein in blood predicts regional atrophy in Huntington disease.
- 2018
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In: Neurology. - 1526-632X. ; 90:8
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Journal article (peer-reviewed)abstract
- Neurofilament light (NfL) protein in blood plasma has been proposed as a prognostic biomarker of neurodegeneration in a number of conditions, including Huntington disease (HD). This study investigates the regional distribution of NfL-associated neural pathology in HD gene expansion carriers.We examined associations between NfL measured in plasma and regionally specific atrophy in cross-sectional (n = 198) and longitudinal (n = 177) data in HD gene expansion carriers from the international multisite TRACK-HD study. Using voxel-based morphometry, we measured associations between baseline NfL levels and both baseline gray matter and white matter volume; and longitudinal change in gray matter and white matter over the subsequent 3 years in HD gene expansion carriers.After controlling for demographics, associations between increased NfL levels and reduced brain volume were seen in cortical and subcortical gray matter and within the white matter. After also controlling for known predictors of disease progression (age and CAG repeat length), associations were limited to the caudate and putamen. Longitudinally, NfL predicted subsequent occipital gray matter atrophy and widespread white matter reduction, both before and after correction for other predictors of disease progression.These findings highlight the value of NfL as a dynamic marker of brain atrophy and, more generally, provide further evidence of the strong association between plasma NfL level, a candidate blood biomarker, and pathologic neuronal change.
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| 17. |
- Lopes, Mariana, et al.
(author)
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Legume beverages from chickpea and lupin, as new milk alternatives
- 2020
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In: Foods. - : MDPI AG. - 2304-8158. ; 9:10
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Journal article (peer-reviewed)abstract
- Recently, milk consumption has been declining and there is a high demand for non-dairy beverages. However, market offers are mainly cereal and nut-based beverages, which are essentially poor in protein (typically, less than 1.5% against the 3.5% in milk) and are not true milk replacers in that sense. In this work, new beverages from different pulses (i.e., pea, chickpea and lupin) were developed using technologies that enable the incorporation of a high level of seed components, with low or no discharge of by-products. Different processing steps were sequentially tested and discussed for the optimization of the sensorial features and stability of the beverage, considering the current commercial non-dairy beverages trends. The lupin beverage protein contents ranged from 1.8% to 2.4% (w/v) and the chickpea beverage varied between 1.0% and 1.5% (w/v). The “milk” yield obtained for the optimized procedure B was 1221 g/100 g of dry seed and 1247 g/100 g of dry seed, for chickpea beverage and lupin beverage, respectively. Sensory results show that chickpea beverage with cooking water has the best taste. All pulses-based beverages are typical non-Newtonian fluids, similarly to current non-dairy alternative beverages. In this respect, the sprouted chickpea beverage, without the cooking water, presents the most pronounced shear-thinning behavior of all formulations.
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| 18. |
- Medronho, Bruno, et al.
(author)
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Silk Fibroin Dissolution in Tetrabutylammonium Hydroxide Aqueous Solution
- 2019
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In: Biomacromolecules. - : American Chemical Society (ACS). - 1525-7797 .- 1526-4602. ; 20, s. 4107-4116
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Journal article (peer-reviewed)abstract
- Bombyx mori L. silk fibroin (SF) is widely used in different areas due to its ability to form durable and resilient materials with notable mechanical properties. However, in some of these applications the dissolution of SF is required, and this is not often straightforward due to its inability to be dissolved in the majority of common solvents. This work reports a novel approach to dissolve SF using 40 wt % aqueous tetrabutylammonium hydroxide, TBAOH(aq), at mild temperature. A thorough rheological study combined with small-angle X-ray scattering is presented to correlate the SF state in solution with changes in the rheological parameters. The scattering data suggest that the SF conformation in TBAOH(aq) is close to a random coil, possibly having some compact domains linked with flexible random chains. The radius of gyration (Rg) and the molecular weight (Mw) were estimated to be ca. 17.5 nm and 450 kDa, respectively, which are in good agreement with previous works. Nevertheless, a lower Mw value was deduced from rheometry (i.e., 321 kDa) demonstrating a low degree of depolymerization during dissolution in comparison to other harsh processes. The transition from a dilute to a semidilute regime coincides with the estimated critical concentration and is marked by the presence of a shear-thinning behavior in the flow curves, violation of the empirical Cox-Merz rule, and an upward increase in the activation energy. This work paves the way toward the development of advanced high-tech SF-based materials. © 2019 American Chemical Society.
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| 19. |
- Melro, Elodie, et al.
(author)
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Revisiting lignin : a tour through its structural features, characterization methods and applications
- 2021
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In: New Journal of Chemistry. - : Royal Society of Chemistry (RSC). - 1144-0546 .- 1369-9261. ; 45:16, s. 6986-7013
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Research review (peer-reviewed)abstract
- Lignin is a complex organic polymer found in the plant cell wall with important biological functions, such as water transport, mechanical support, and resistance to various stresses. It is considered the second most abundant biopolymer on earth and the largest natural source of aromatics. Despite being annually co-produced in massive amounts, during cellulose fragmentation in the pulp industry and ethanol biorefinery, it is clearly undervalued; most of it is discarded or burned as fuel for energy production and, so far, only ca. 1-2% of lignin has been utilized as a high-value product. This underuse makes lignin the future resource of choice to produce green fuels and a wide range of added-value biomaterials and chemicals, which can contribute to the transition to more sustainable industries. However, its great variability between plant families combined with its complex and chemically inert structure is challenging researchers who seek for strategies regarding its valorization. With this scope, several different approaches have emerged regarding the development of better and efficient isolation methods, purification and characterization techniques, and improved methodologies for lignin chemical modification and blending with other compounds. These improvements represent important opportunities for the creation of value-added lignin-based biopolymers and materials and some have already shown potential to be scaled up. All these aspects are pedagogically introduced and discussed in this review.
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| 20. |
- Richards, Stephen, et al.
(author)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Journal article (peer-reviewed)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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| 21. |
- Rosa, Fábio F., et al.
(author)
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Direct reprogramming of fibroblasts into antigen-presenting dendritic cells
- 2018
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In: Science Immunology. - : American Association for the Advancement of Science (AAAS). - 2470-9468. ; 3:30
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Journal article (peer-reviewed)abstract
- Ectopic expression of transcription factors has been used to reprogram differentiated somatic cells toward pluripotency or to directly reprogram them to other somatic cell lineages. This concept has been explored in the context of regenerative medicine. Here, we set out to generate dendritic cells (DCs) capable of presenting antigens from mouse and human fibroblasts. By screening combinations of 18 transcription factors that are expressed in DCs, we have identified PU.1, IRF8, and BATF3 transcription factors as being sufficient to reprogram both mouse and human fibroblasts to induced DCs (iDCs). iDCs acquire a conventional DC type 1-like transcriptional program, with features of interferon-induced maturation. iDCs secrete inflammatory cytokines and have the ability to engulf, process, and present antigens to T cells. Furthermore, we demonstrate that murine iDCs generated here were able to cross-present antigens to CD8+ T cells. Our reprogramming system should facilitate better understanding of DC specification programs and serve as a platform for the development of patient-specific DCs for immunotherapy.
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| 22. |
- Rosa, Fábio F, et al.
(author)
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Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells
- 2022
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In: Science Immunology. - : American Association for the Advancement of Science (AAAS). - 2470-9468. ; 7:69, s. 1-18
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Journal article (peer-reviewed)abstract
- Type 1 conventional dendritic cells (cDC1s) are rare immune cells critical for the induction of antigen-specific cytotoxic CD8+ T cells, although the genetic program driving human cDC1 specification remains largely unexplored. We previously identified PU.1, IRF8, and BATF3 transcription factors as sufficient to induce cDC1 fate in mouse fibroblasts, but reprogramming of human somatic cells was limited by low efficiency. Here, we investigated single-cell transcriptional dynamics during human cDC1 reprogramming. Human induced cDC1s (hiDC1s) generated from embryonic fibroblasts gradually acquired a global cDC1 transcriptional profile and expressed antigen presentation signatures, whereas other DC subsets were not induced at the single-cell level during the reprogramming process. We extracted gene modules associated with successful reprogramming and identified inflammatory signaling and the cDC1-inducing transcription factor network as key drivers of the process. Combining IFN-γ, IFN-β, and TNF-α with constitutive expression of cDC1-inducing transcription factors led to improvement of reprogramming efficiency by 190-fold. hiDC1s engulfed dead cells, secreted inflammatory cytokines, and performed antigen cross-presentation, key cDC1 functions. This approach allowed efficient hiDC1 generation from adult fibroblasts and mesenchymal stromal cells. Mechanistically, PU.1 showed dominant and independent chromatin targeting at early phases of reprogramming, recruiting IRF8 and BATF3 to shared binding sites. The cooperative binding at open enhancers and promoters led to silencing of fibroblast genes and activation of a cDC1 program. These findings provide mechanistic insights into human cDC1 specification and reprogramming and represent a platform for generating patient-tailored cDC1s, a long-sought DC subset for vaccination strategies in cancer immunotherapy.
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| 23. |
- São José, José Manuel Sousa, et al.
(author)
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Ageism in Health Care : A Systematic Review of OperationalDefinitions and Inductive Conceptualizations
- 2019
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In: The Gerontologist. - : Oxford University Press. - 0016-9013 .- 1758-5341. ; 59:2, s. E98-E108
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Research review (peer-reviewed)abstract
- Purpose:International and national bodies have identified tackling ageism in health care as an urgent goal. However, health professionals, researchers, and policy makers recognize that it is not easy to identity and fight ageism in practice, as the identification of multiple manifestations of ageism is dependent on the way it is defined and operationalized. This article reports on a systematic review of the operational definitions and inductive conceptualizations of ageism in the context of health care.Design and Methods:We reviewed scientific articles published from January 1995 to June 2015 and indexed in the electronic databases Web of Science, PubMed, and Cochrane. Electronic searches were complemented with visual scanning of reference lists and hand searching of leading journals in the field of ageing and social gerontology.Results:The review reveals that the predominant forms of operationalization and inductive conceptualization of ageism in the context of health care have neglected some components of ageism, namely the self-directed and implicit components. Furthermore, the instruments used to measure ageism in health care have as targets older people in general, not older patients in particular.Implications:The results have important implications for the advancement of research on this topic, as well as for the development of interventions to fight ageism in practice. There is a need to take into account underexplored forms of operationalization and inductive conceptualizations of ageism, such as self-directed ageism and implicit ageism. In addition, ageism in health care should be measured by using context-specific instruments.
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| 24. |
- Silvério-Alves, Rita, et al.
(author)
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GATA2 mitotic bookmarking is required for definitive haematopoiesis
- 2023
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In: Nature Communications. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- In mitosis, most transcription factors detach from chromatin, but some are retained and bookmark genomic sites. Mitotic bookmarking has been implicated in lineage inheritance, pluripotency and reprogramming. However, the biological significance of this mechanism in vivo remains unclear. Here, we address mitotic retention of the hemogenic factors GATA2, GFI1B and FOS during haematopoietic specification. We show that GATA2 remains bound to chromatin throughout mitosis, in contrast to GFI1B and FOS, via C-terminal zinc finger-mediated DNA binding. GATA2 bookmarks a subset of its interphase targets that are co-enriched for RUNX1 and other regulators of definitive haematopoiesis. Remarkably, homozygous mice harbouring the cyclin B1 mitosis degradation domain upstream Gata2 partially phenocopy knockout mice. Degradation of GATA2 at mitotic exit abolishes definitive haematopoiesis at aorta-gonad-mesonephros, placenta and foetal liver, but does not impair yolk sac haematopoiesis. Our findings implicate GATA2-mediated mitotic bookmarking as critical for definitive haematopoiesis and highlight a dependency on bookmarkers for lineage commitment.
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| 25. |
- Zimmermannova, Olga, et al.
(author)
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Cell Fate Reprogramming in the Era of Cancer Immunotherapy
- 2021
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In: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 12
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Research review (peer-reviewed)abstract
- Advances in understanding how cancer cells interact with the immune system allowed the development of immunotherapeutic strategies, harnessing patients’ immune system to fight cancer. Dendritic cell-based vaccines are being explored to reactivate anti-tumor adaptive immunity. Immune checkpoint inhibitors and chimeric antigen receptor T-cells (CAR T) were however the main approaches that catapulted the therapeutic success of immunotherapy. Despite their success across a broad range of human cancers, many challenges remain for basic understanding and clinical progress as only a minority of patients benefit from immunotherapy. In addition, cellular immunotherapies face important limitations imposed by the availability and quality of immune cells isolated from donors. Cell fate reprogramming is offering interesting alternatives to meet these challenges. Induced pluripotent stem cell (iPSC) technology not only enables studying immune cell specification but also serves as a platform for the differentiation of a myriad of clinically useful immune cells including T-cells, NK cells, or monocytes at scale. Moreover, the utilization of iPSCs allows introduction of genetic modifications and generation of T/NK cells with enhanced anti-tumor properties. Immune cells, such as macrophages and dendritic cells, can also be generated by direct cellular reprogramming employing lineage-specific master regulators bypassing the pluripotent stage. Thus, the cellular reprogramming toolbox is now providing the means to address the potential of patient-tailored immune cell types for cancer immunotherapy. In parallel, development of viral vectors for gene delivery has opened the door for in vivo reprogramming in regenerative medicine, an elegant strategy circumventing the current limitations of in vitro cell manipulation. An analogous paradigm has been recently developed in cancer immunotherapy by the generation of CAR T-cells in vivo. These new ideas on endogenous reprogramming, cross-fertilized from the fields of regenerative medicine and gene therapy, are opening exciting avenues for direct modulation of immune or tumor cells in situ, widening our strategies to remove cancer immunotherapy roadblocks. Here, we review current strategies for cancer immunotherapy, summarize technologies for generation of immune cells by cell fate reprogramming as well as highlight the future potential of inducing these unique cell identities in vivo, providing new and exciting tools for the fast-paced field of cancer immunotherapy.
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| 26. |
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| 27. |
- Zimmermannova, Olga, et al.
(author)
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Restoring tumor immunogenicity with dendritic cell reprogramming
- 2023
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In: Science Immunology. - 2470-9468. ; 8:85
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Journal article (peer-reviewed)abstract
- Decreased antigen presentation contributes to the ability of cancer cells to evade the immune system. We used the minimal gene regulatory network of type 1 conventional dendritic cells (cDC1) to reprogram cancer cells into professional antigen-presenting cells (tumor-APCs). Enforced expression of the transcription factors PU.1, IRF8, and BATF3 (PIB) was sufficient to induce the cDC1 phenotype in 36 cell lines derived from human and mouse hematological and solid tumors. Within 9 days of reprogramming, tumor-APCs acquired transcriptional and epigenetic programs associated with cDC1 cells. Reprogramming restored the expression of antigen presentation complexes and costimulatory molecules on the surfaces of tumor cells, allowing the presentation of endogenous tumor antigens on MHC-I and facilitating targeted killing by CD8 + T cells. Functionally, tumor-APCs engulfed and processed proteins and dead cells, secreted inflammatory cytokines, and cross-presented antigens to naïve CD8 + T cells. Human primary tumor cells could also be reprogrammed to increase their capability to present antigen and to activate patient-specific tumor-infiltrating lymphocytes. In addition to acquiring improved antigen presentation, tumor-APCs had impaired tumorigenicity in vitro and in vivo. Injection of in vitro generated melanoma-derived tumor-APCs into subcutaneous melanoma tumors delayed tumor growth and increased survival in mice. Antitumor immunity elicited by tumor-APCs was synergistic with immune checkpoint inhibitors. Our approach serves as a platform for the development of immunotherapies that endow cancer cells with the capability to process and present endogenous tumor antigens.
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